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Yorodumi- PDB-6x7c: BRD4 Bromodomain 1 in complex with multi-action inhibitor SRX3212 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x7c | ||||||
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Title | BRD4 Bromodomain 1 in complex with multi-action inhibitor SRX3212 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / BRD4 / PI3K / CDK4/6 | ||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Vann, K.R. / Kutateladze, T.G. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Design of thienopyranone-based BET inhibitors that bind multiple synthetic lethality targets. Authors: Vann, K.R. / Pal, D. / Morales, G.A. / Burgoyne, A.M. / Durden, D.L. / Kutateladze, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x7c.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x7c.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 6x7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/6x7c ftp://data.pdbj.org/pub/pdb/validation_reports/x7/6x7c | HTTPS FTP |
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-Related structure data
Related structure data | 6x7bC 6x7dC 3mxfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15854.252 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-KV9 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 40% PEG 3350, 0.2 M Pottassium thiocyanate pH 7.5, and 4% 1,1,1,3,3,3-Hexafluoro-2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 18, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 3407 / % possible obs: 94.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 25.92 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.049 / Rrim(I) all: 0.079 / Χ2: 0.955 / Net I/σ(I): 15.5 / Num. measured all: 7734 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mxf Resolution: 2.7→23.005 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 27.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 33.58 Å2 / Biso mean: 23.7046 Å2 / Biso min: 14.07 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→23.005 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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